Contacts of the strand formed by residues 231 - 237 (chain B) in PDB entry 3RAW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B VAL* 5.1 2.0 - - - +
138B ASP* 4.2 8.2 - - + +
142B GLY 3.4 16.2 - - - -
143B HIS 3.8 1.3 - - - -
144B LEU* 3.4 61.0 + - + +
187B ILE* 4.0 13.4 - - + +
188B ILE 3.0 25.3 + - - +
189B ARG 4.0 0.2 - - - -
190B ASN* 3.5 19.2 + - + +
227B ASN* 4.2 0.9 - - - -
228B PHE* 2.7 49.6 + + + +
229B HIS* 3.9 10.5 - - + -
230B GLY* 1.3 77.1 - - - +
232B MET* 1.3 61.3 + - - +
233B CYS* 3.5 6.8 - - - -
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Residues in contact with MET 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B ILE* 2.8 38.5 + - + +
189B ARG 5.3 0.6 + - - -
195B ARG* 3.5 36.1 - - + +
198B ALA* 3.9 20.2 - - + -
199B ARG* 4.2 24.7 - - + +
202B ILE* 3.6 28.9 - - + -
225B TRP* 3.9 21.5 - - + -
226B PHE 3.5 7.9 - - - +
227B ASN* 4.0 26.0 - - + +
230B GLY 3.4 2.2 + - - -
231B HIS* 1.3 71.1 - - - +
233B CYS* 1.3 59.9 + - - +
234B ILE* 5.2 0.9 - - + -
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Residues in contact with CYS 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU* 4.4 5.6 - - - -
185B LEU* 4.2 7.0 - - + -
186B LYS 3.1 6.7 - - - +
187B ILE* 4.2 27.8 - - - -
202B ILE* 5.0 0.5 - - - +
225B TRP* 3.1 6.2 - - - +
226B PHE* 2.8 70.5 + - + +
228B PHE* 4.0 8.1 - - - -
231B HIS* 3.5 17.0 - - - -
232B MET* 1.3 76.3 - - - +
234B ILE* 1.3 63.0 + - - +
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Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B ALA 3.7 1.0 - - - +
185B LEU* 3.6 3.7 - - - -
186B LYS* 3.0 37.2 + - + +
188B ILE* 5.6 1.6 - - + -
198B ALA* 4.4 10.8 - - + +
201B GLU* 3.6 34.8 - - + +
202B ILE* 3.7 30.5 - - + -
205B LEU* 4.3 1.8 - - + -
222B MET* 3.6 30.5 - - + -
224B ASP 3.6 2.9 - - - +
225B TRP* 4.5 0.2 - - + -
232B MET 5.2 2.0 - - - -
233B CYS* 1.3 80.3 - - - +
235B ALA* 1.3 62.4 + - - +
236B PHE* 3.4 30.4 - - + -
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B TYR* 4.0 25.4 - - + +
183B VAL* 4.5 6.7 - - + -
184B ALA 3.5 5.6 - - - +
185B LEU* 3.9 16.0 - - + +
222B MET* 3.3 8.7 - - - +
223B SER* 2.8 40.6 + - - +
224B ASP* 2.8 18.5 + - + +
226B PHE* 5.5 0.8 - - + -
234B ILE* 1.3 72.7 - - - +
236B PHE* 1.3 56.2 + - - +
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Residues in contact with PHE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B 3RA 3.7 50.5 - + + -
183B VAL* 3.2 10.4 - - - +
184B ALA* 2.8 34.3 + - + +
186B LYS* 4.0 16.6 - - + -
201B GLU* 4.4 5.8 - - - -
205B LEU* 3.7 27.4 - - + -
220B VAL* 3.7 27.6 - - + -
221B LEU 3.3 17.7 - - - +
222B MET* 3.9 5.8 - - + -
223B SER* 4.2 5.4 - - - -
234B ILE* 3.4 37.9 - - + -
235B ALA* 1.3 72.7 - - - +
237B GLU* 1.3 62.7 + - - +
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B 3RA 3.7 8.8 - - - -
182B GLN 4.7 4.9 - - - -
183B VAL* 5.3 0.9 - - - -
220B VAL* 5.9 0.5 - - - +
221B LEU* 3.2 31.4 + - + +
223B SER* 4.6 2.9 + - - -
236B PHE* 1.3 75.5 - - - +
238B LEU* 1.3 65.7 + - - +
239B LEU* 3.5 19.1 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il